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Due to its important geographic location and unique environment, the Gansu and Qinghai region in China has been witnessing the emergence and development of Chinese civilization. This previously neglected region has recently been attracting people's attention. Existing studies have been mainly aiming to relate the spatiotemporal distributions of settlements to environmental changes. However, they generally fail to consider the evolution of social organizations and its role in impacting the spatiotemporal variations of prehistoric settlements. In this paper, we analyzed the spatiotemporal distribution and rank-size of prehistoric settlements in the Gansu-Qinghai region based on GIS analytical methods and reconstructed the process of cultural inheritance and social evolution. The examined chronological periods were demonstrated to be concomitant with different settlement development patterns, and most settlements in an older period were abandoned in the subsequently younger period, indicating poor inheritance. The occurrence of a three-tier regional settlement system during the late Yangshao–Majiayao period indicates fundamental changes in social organization, which is possibly related to the rise of a chiefdom-level society. Such a regional social stratification was intensified during the Qijia period, when a four-tier settlement system emerged. However, the complexity of the settlement system got weakened during the Bronze Age, as is indicated by the lowered hierarchy of the settlement system. The drying and cooling climatic event rendered nomadism the prevalent subsistence among the humans in the Gansu and Qinghai region who used to survive by participating in agricultural activities. • Use Gis to analyse the settlement morophology. • Use the rank-size to analyse the settlement system. • Development of trajectories settlement system. [ABSTRACT FROM AUTHOR]